DNA methylome analysis using short bisulfite sequencing data

2012 ◽  
Vol 9 (2) ◽  
pp. 145-151 ◽  
Author(s):  
Felix Krueger ◽  
Benjamin Kreck ◽  
Andre Franke ◽  
Simon R Andrews
Keyword(s):  
Bisulfite Sequencing ◽  
Sequencing Data ◽  
Dna Methylome ◽  
Methylome Analysis ◽  
Bisulfite Sequencing Data

scholarly journals BiSulfite Bolt: A bisulfite sequencing analysis platform

GigaScience ◽  
2021 ◽  
Vol 10 (5) ◽  
Author(s):  
Colin Farrell ◽  
Michael Thompson ◽  
Anela Tosevska ◽  
Adewale Oyetunde ◽  
Matteo Pellegrini
Keyword(s):  
Data Aggregation ◽  
Bisulfite Sequencing ◽  
Low Complexity ◽  
Sequencing Analysis ◽  
Command Line ◽  
Sequencing Data ◽  
Bisulfite Sequencing Data ◽  
Analysis Platform ◽  
Python Package ◽  
Bisulfite Sequencing Analysis

Abstract Background Bisulfite sequencing is commonly used to measure DNA methylation. Processing bisulfite sequencing data is often challenging owing to the computational demands of mapping a low-complexity, asymmetrical library and the lack of a unified processing toolset to produce an analysis-ready methylation matrix from read alignments. To address these shortcomings, we have developed BiSulfite Bolt (BSBolt), a fast and scalable bisulfite sequencing analysis platform. BSBolt performs a pre-alignment sequencing read assessment step to improve efficiency when handling asymmetrical bisulfite sequencing libraries. Findings We evaluated BSBolt against simulated and real bisulfite sequencing libraries. We found that BSBolt provides accurate and fast bisulfite sequencing alignments and methylation calls. We also compared BSBolt to several existing bisulfite alignment tools and found BSBolt outperforms Bismark, BSSeeker2, BISCUIT, and BWA-Meth based on alignment accuracy and methylation calling accuracy. Conclusion BSBolt offers streamlined processing of bisulfite sequencing data through an integrated toolset that offers support for simulation, alignment, methylation calling, and data aggregation. BSBolt is implemented as a Python package and command line utility for flexibility when building informatics pipelines. BSBolt is available at https://github.com/NuttyLogic/BSBolt under an MIT license.

scholarly journals A Bayesian Approach for Analysis of Whole-Genome Bisulfite Sequencing Data Identifies Disease-Associated Changes in DNA Methylation

Genetics ◽  
2017 ◽  
Vol 205 (4) ◽  
pp. 1443-1458 ◽  
Author(s):  
Owen J. L. Rackham ◽  
Sarah R. Langley ◽  
Thomas Oates ◽  
Eleni Vradi ◽  
Nathan Harmston ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Bayesian Approach ◽  
Bisulfite Sequencing ◽  
Whole Genome ◽  
Sequencing Data ◽  
Whole Genome Bisulfite Sequencing ◽  
Genome Bisulfite Sequencing ◽  
Bisulfite Sequencing Data

scholarly journals GBSA: a comprehensive software for analysing whole genome bisulfite sequencing data

2012 ◽  
Vol 41 (4) ◽  
pp. e55-e55 ◽  
Author(s):  
Touati Benoukraf ◽  
Sarawut Wongphayak ◽  
Luqman Hakim Abdul Hadi ◽  
Mengchu Wu ◽  
Richie Soong
Keyword(s):  
Bisulfite Sequencing ◽  
Whole Genome ◽  
Sequencing Data ◽  
Whole Genome Bisulfite Sequencing ◽  
Genome Bisulfite Sequencing ◽  
Bisulfite Sequencing Data

scholarly journals MethGo: a comprehensive tool for analyzing whole-genome bisulfite sequencing data

BMC Genomics ◽  
2015 ◽  
Vol 16 (Suppl 12) ◽  
pp. S11 ◽  
Author(s):  
Wen-Wei Liao ◽  
Ming-Ren Yen ◽  
Evaline Ju ◽  
Fei-Man Hsu ◽  
Larry Lam ◽  
...  
Keyword(s):  
Bisulfite Sequencing ◽  
Whole Genome ◽  
Sequencing Data ◽  
Whole Genome Bisulfite Sequencing ◽  
Genome Bisulfite Sequencing ◽  
Bisulfite Sequencing Data

RRBS-Analyser: A Comprehensive Web Server for Reduced Representation Bisulfite Sequencing Data Analysis

2013 ◽  
Vol 34 (12) ◽  
pp. 1606-1610 ◽  
Author(s):  
Tao Wang ◽  
Qi Liu ◽  
Xianfeng Li ◽  
Xiaobing Wang ◽  
Jinchen Li ◽  
...  
Keyword(s):  
Data Analysis ◽  
Bisulfite Sequencing ◽  
Web Server ◽  
Sequencing Data ◽  
Reduced Representation ◽  
Reduced Representation Bisulfite Sequencing ◽  
Bisulfite Sequencing Data ◽  
Sequencing Data Analysis

scholarly journals wg-blimp: an end-to-end analysis pipeline for whole genome bisulfite sequencing data

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Marius Wöste ◽  
Elsa Leitão ◽  
Sandra Laurentino ◽  
Bernhard Horsthemke ◽  
Sven Rahmann ◽  
...  
Keyword(s):  
Bisulfite Sequencing ◽  
Whole Genome ◽  
Sequencing Data ◽  
Analysis Pipeline ◽  
Whole Genome Bisulfite Sequencing ◽  
Genome Bisulfite Sequencing ◽  
Bisulfite Sequencing Data ◽  
End To End
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